softThreshold: softThreshold.Seurat

In WilsonImmunologyLab/LinQView: Integrate information from both transcriptome and cell surface protein signals to better identify cell heterogeneity

Description

softThreshold

Usage

## S3 method for class 'Seurat'
softThreshold(object = NULL, sealing = 10)

## Default S3 method:
softThreshold(object = NULL, sealing = 10)

softThreshold(object, ...)

Arguments

object	(For Seurat) Seurat object
sealing	(For default) the sealing point of mitochondrial gene threshold, for 10X data we suggest use 10 percent
data	(For default) Array of mito percent

Details

determine the soft threshold of percentage of mitochondrial gene. The criteria is: for each sample, we only keep the 95 percent cells with lowest percent of mito genes. If the cell quality is too bad, we use 10 percent as a sealing threshold

WilsonImmunologyLab/LinQView documentation built on Jan. 3, 2022, 10 p.m.